ClusterDE

a post-clustering differential expression method

Carson Zhang

June 29, 2024

Outline

  • Context
    • Why and when would we use this?
    • What are the problems with existing methods or analysis procedures?
  • Method
    • What is ClusterDE?
    • How does it avoid the problems of other methods?
  • Examples
    • How would you use ClusterDE?
  • Extensions
    • Variations on the ClusterDE method

Context

Differential Expression

Example of a subtitle

We can create unordered lists:

  • first item
    • A sub item

Or ordered lists

  1. Ordered list first item
    1. Nested list item

Or bold, italic, or URL text.

Method

Synthetic null generation

Inline mode: \(c^2 = a^2 + b^2\)

Display mode:

\[x = \frac{-b \pm \sqrt{b^2 - 4ac}}{2a}\]

Clustering

DE analysis (hypothesis testing)

FDR control

Example

Columns

We could also split content between two columns:

Left column

Right column

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Code Highlighting

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For discontinuous highlighting, use line1, line2, ... (1, 4).

To highlight lines in a progressive manner, use range1|range2 (|6-8|1,4|).

import numpy as np
import matplotlib.pyplot as plt

r = np.arange(0, 2, 0.01)
theta = 2 * np.pi * r
fig, ax = plt.subplots(subplot_kw={'projection': 'polar'})
ax.plot(theta, r)
ax.set_rticks([0.5, 1, 1.5, 2])
ax.grid(True)
plt.show()

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    chalkboard: true